Báo cáo khoa học: "Controlled Authoring of Biological Experiment Reports" docx

Controlled Authoring of Biological Experiment Reports
Caroline Brun
Xerox Research Centre Europe

Eric Fanchon
Institut de Biologic Structurale

Abstract
We give a demonstration of an application of
XRCE's controlled text authoring system MDA to
biological experiment reports. This work is the
result of a collaboration between XRCE's Docu-
ment Content Models team, CNRS's Institut de
Biologic Structurale, and Protein'eXpert, a com-
pany specialized in biotechnology based in
Grenoble. We start with a brief presentation of the
partners involved and their respective goals. We
then give some technical background on the MDA
system. Some novel features of the application are
discussed, in particular how MDA can be used for
integrating the formalization of an experimental
protocol with its associated textual documenta-
tion.
1 Partners involved
1.1 Protein'eXpert
Whereas the human genome sequencing has now been
completed, the formidable task remains of understand-
ing the function of proteins encoded by genes. For this
reason, the production of
recombinant proteins
has

become an essential aspect of biomedical and biotech-
nology research, that is, exploratory therapeutic re-
search, functional and structural studies. Genes are
coding sequences of DNA molecules and are the tem-
plates from which proteins are synthesized.
Proteins are long linear molecules, which fold into a
well-defined 3-dimensional structure. The structure of
a protein determines its biological function.
The synthesis of proteins from genes is performed by
the complex molecular machinery present in living
cells. Recombinant DNA technology
is a set of proce-
dures that allow the production of a protein from a
given organism by another organism, which can be
easily manipulated and cultured. In appropriate condi-
tions these host cells are forced to synthesize the pro-
tein that has been artificially incorporated. Thus, by
Marc Dymetman
Xerox Research Centre Europe

Stanistas
Lhomme
Protein'eXpert

transferring a gene of interest into an organism such as
Escherichia coli
it is possible to obtain large quantities
of the protein corresponding to the gene (Baneyx 99).
Each protein has a specific behavior and many pa-
rameters can vary

(Stevens 2000). Protein'eXpert
1
has
developed an expertise to determine optimal produc-
tion conditions for recombinant proteins, and it pro-
vides several products and services in this field. One
of these services is called the
feasibility study
which is
a complete and standardized protein production study
including cloning, expression and solubility tests, cell
fractionation, purification, refolding assay (when nec-
essary), quality control and delivery of 1-10 mg of
soluble proteins. The feasibility study has been de-
signed to optimize protein production protocols and to
give comprehensive information about protein synthe-
sis and purification conditions. By the end of the
study, proteins are delivered with a complete produc-
tion protocol, an expression plasmid, and a solution
proposal if the protein is difficult to express. The fea-
sibility study is carried out by a laboratory technician
under the guidance of a project manager. The techni-
cian performs all the experiments and the manager
writes the final report. This study follows a complex
protocol with several alternatives and potential revi-
sions of previous steps.
The experimental part lasts
for about six to ten weeks and the authoring takes
several hours.
1.2 DCM

-
XRCE
The DCM
2
(Document Content Models)
team is part
of the Content Analysis
3
area at XRCE , and explores
formalisms and techniques for specifying, manipulat-
ing and exploiting the semantic structures of docu-
ments, seen as global and cohesive objects. One of the
DCM projects is called MDA (Multilingual Document
Authoring). MDA is an interactive system for assist-
ing monolingual writers in the production of multilin-
1
/>2
/>analysis/dcm/
3
/>4
/>
195
gual documents. This tool extends conventional syn-
tax-driven SGML or XML editors so that semantic
choices down to the level of words are possible when
authoring the document content. In addition,
depend-
encies between two distant parts of the document can
be specified in such a way that a change in one part of
the document is reflected in a change in some other

part of the document (long distance dependencies).
The author's choices have
language-independent
meanings
(example in the case of a drug leaflet:
choosing between a
tablet
and a
syrup),
which are
automatically rendered in any of the languages known
to the system, along with their
grammatical conse-
quences
on the surrounding text. Although the author
is not explicitly following standards, the text produced
by the system is implicitly controlled both:
Syntactically and stylistically: the choice of the stan-
dard terminology for expressing a given notion is un-
der system control, as is the choice between
grammatical variants (such as active/passive sen-
tences) for expressing a given information;
Semantically: the consequences of a choice some-
where are reflected across the whole document, the
author cannot forget to provide some information that
the system requires, dependencies between semantic
parameters (for instance,
pregnancy
and person
gen-

der)
can be described.
MDA is an instance of an
interactive natural language
generation
system. Early systems such as DRAFTER
(Paris et al. 1995), allow the user to specify interac-
tively an internal semantic representation, from which
textual realizations can be produced automatically
through a generation process. More recently, in the
WYSIWYM [What You See Is What You Mean] ap-
proach, (Power and Scott 98) introduced the idea of
using the textual realization itself as the basis for in-
teracting with and updating the internal representa-
tion.
A similar approach was adopted in GF
[Grammatical Framework] (Ranta 1999-), a system
which has its roots in interactive mathematical proof
editors, and which provides the core model for MDA.
While GF is based on higher-order constructive type
theory formulation of well-formed semantic represen-
tation and has its own specific grammatical realization
formalism, MDA uses a single formalism
(Definite
Clause Grammars)
both for the formulation of well-
formed semantic representation and of its textual re-
alization. Both GF and MDA stress the importance of
a formal specification of the well-fbrmedness of the
semantic representation

underlying the textual realiza-
tion, while (Power and Scott 98) concentrates on the
formal
connections between the semantic representa-
tion and the textual realization.
5
The MDA home page
6
gives an overview of the capa-
bilities and uses of the system, along with related pa-
pers, as well as a demo in the area of pharmaceutical
documents.'
2 Aims of the collaboration
Beyond the aspects of
standardization and quality
improvements of their reports,
which was a primary
requirement, Protein'eXpert was interested in
produc-
ing the experiment reports more quickly,
since writing
such reports is a time consuming task. Moreover, Pro-
tein'eXpert wanted to allow technicians, who run the
experiments, to author at least some parts of the final
reports themselves. Since MDA guides the author, this
task can be given to people less experienced in writing
documents without risking a decrease in quality, both
at the level of the semantic dependencies to be re-
spected, and at the level of the proper English expres-
sions to be used (French being the commonly used

language at Protein'eXpert).
From XRCE-DCM's viewpoint, the main objectives
of the collaboration were to confirm the value of our
previously developed methodology for describing the
content and form of technical documents by working
in a completely new domain, as well as to get an un-
derstanding of the potential of MDA-controlled au-
thoring in
a previously untouched business area:
experimental protocols and documentation.
While these were the initial goals of the collaboration,
an interesting and unexpected outcome of performing
the concrete work gradually led us to
a novel, and
more general, perspective.
We noticed the existence
of a strong parallelism between the experimental pro-
tocol (what experimental steps to perform with which
parameters, what decisions to take, how these deci-
sions affect the next steps) and the structure and de-
pendencies in the written report. It was then exciting
to discover that the computational model underlying
MDA was very adapted, not only to the description of
the written report, but also to the fine-grained fbrmal-
ization of the experimental protocol itself In this way,
we have gradually moved to a view of MDA as a con-
venient tool for integrating the formalization of the
5
This difference has several decisive theoretical and practi-
cal consequences, in particular for the connection between

these systems and XML-based authoring, as well as for the
definability of such notions as
life/death
of authoring
choices (Dymetman 2002).
6
/>analvsis/dcm/mda.en.html
7
/>analysis/dcm/demo/mda-demo.html
196
experimental protocol with its associated textual
documentation.
3 The realization
3.1 Design
The first step of prototype design was to specify the
structure and content of the experiment reports. With
the help of the grammar writers, the biological experts
produced guidelines, both at the level of semantic con-
tent and of the textual expressions to be used. It was
then followed by DCM formalizing these descriptions
and implementing them in the MDA formalism. De-
tails about this formalism are given in (Dymetman et
al. 2000) and (Brun et al. 2000).
During the formalization and implementation phase,
XRCE used its previously developed methodology of
first modeling the document macro-structure (similar
to a DTD
8
), then its context-free micro-structure (what
types of content choices are possible at a given point

in the document), and finally the dependencies be-
tween different content elements (example: some ex-
perimental observations lead to certain obligatory
choices concerning the sequel of the experiment).
To perform this formalization/implementation phase, a
biological expert and a grammar developer worked
in
tandem
for about 40 person-days.
A side-effect benefit of such a collaboration between
biologists and computational linguists is the opportu-
nity it offers to formally analyze the content of a set of
documents to extract domain-specific knowledge: this
decision leads to that result, etc.
3.2 Implementation
The generic components of the system consist in an
interaction kernel, written in Prolog, connected with a
Java-based GUI. The interaction kernel interprets do-
main-specific grammars (written in a notational vari-
ant of Definite Clause Grammars), which are used
both for the specification of well-formed document
content as well as for the textual realizations of this
content. In the case of the reports being discussed, we
developed grammars for English as well as French
realization, each containing about 380 rules.
3.3 A Glance at the Interface
The following figures show some screenshots of the
prototype in use. The author interacts with menus as-
sociated with underlined items and may also enter free
text in dedicated boxes.

8
DTD stands for Document Type Definition
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Fig.2: Consequences of a semantic choice.
4 Results
The collaboration already led to large-scale English
and French grammars for the interactive authoring of
biological experiments reports.
The formalization process has also been extremely
valuable in inducing Protein'eXpert to be more pre-
cise in the conditions under which a certain textual
expression is produced or a certain justification is
given for a decision made.
197
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The analysis of the gels allows to select one clone for the tag and. the two bacterial stxains.
The detection on a SD 5-Page shows that the expression of the target protein
is bacterial strain dependent The pxotein expression is indeed more detectable
in the bacterial strain BL21(DE3)
The detection on a SD 5-PAGE gel shows that the degradation of the target protein

is bacterial strain dependent Whatever the tag position, the protein degradation is indeed more detectable
in the bacterial strain BL21(DE3)
The clones 5 and I were interesting. Nevertheless, despite a lower expression than the clone
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-
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Fig.3: Analysis of a picture via a table and interactive
generation of explanations.
Although this formalization process has a cost, this
cost is amply repaid by the consistency and quality of
the documents produced, a result that would be diffi-
cult to obtain if production of the reports where to be
done manually under time-pressure.
Another interesting aspect of the collaboration is that
the document class (reports on the production of re-
combinant proteins) has been designed without being
constrained by a huge corpus of legacy documents to
be accommodated. The MDA methodology is then
useful, not only for producing a controlled authoring
system, but as a systematic and effective way of ap-
proaching the design of new documents where a high
degree of formal precision is needed.
One unforeseen and innovative outcome of the joint

work has been the possibility of formalizing certain
decisions taken by the biological engineers on the
basis of raw experimental data. It is now possible for
the author to input simply certain visual features of an
image (a gel in biological terminology), and the au-
thoring system is able to take some decisions auto-
matically (relative to such things as a choice of
bacterial strain to express the protein) and also
to pro-
vide textual justifications for these decisions (see Fig
.3)•
9
9
The author however has the possibility of bypassing these
decisions if he does not agree.
5 Evaluation and Conclusion
The prototype for experimental reports is now under
evaluation
in situ
at Protein'eXpert. First results indi-
cate that the system clearly improves the quality and
speed of report production. About 30 minutes are
needed for authoring a report using the system, instead
of several hours previously. The
in situ
evaluation
also made us discover an unexpected side of the MDA
system: its didactical aspect. The system works as a
self-explaining tool since the logical consequences of
a given choice at a given authoring state are immedi-

ately visible to the user. Another interesting feature is
that in a multi-author context (several people contrib-
uting to a given document) MDA can provide a com-
mon working frame, by allowing technicians working
on different facets of the experiment to contribute to
the same report.
Finally, and perhaps most interestingly, we already
mentioned a new perspective opened by the current
work:
MDA can be viewed as a tool 'Or integrating
formalization of the experimental protocol with its
written documentation.
The main problem identified at this point lies in the
reusability and adaptability of the prototype for new
classes of experiments/documents in the same domain.
This is a crucial point that will be addressed in the
next phases of development, in particular through
work on support tools for the grammar developer.
References
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Recombinant protein expression in Es-
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XML and
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